Journal article

Impact of regulatory variation across human iPSCs and differentiated cells

Nicholas E Banovich, Yang I Li, Anil Raj, Michelle C Ward, Peyton Greenside, Diego Calderon, Po Yuan Tung, Jonathan E Burnett, Marsha Myrthil, Samantha M Thomas, Courtney K Burrows, Irene Gallego Romero, Bryan J Pavlovic, Anshul Kundaje, Jonathan K Pritchard, Yoav Gilad

GENOME RESEARCH | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2018

Abstract

Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility, and DNA methylation. Our analysis focused on a comp..

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University of Melbourne Researchers

Grants

Awarded by NIH


Awarded by EMBO Long-Term Fellowship


Awarded by NATIONAL CANCER INSTITUTE


Awarded by NATIONAL HEART, LUNG, AND BLOOD INSTITUTE


Awarded by NATIONAL HUMAN GENOME RESEARCH INSTITUTE


Awarded by NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES


Awarded by NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES


Awarded by NATIONAL INSTITUTE OF MENTAL HEALTH


Awarded by NATIONAL INSTITUTE ON AGING


Awarded by NATIONAL LIBRARY OF MEDICINE


Funding Acknowledgements

We thank members of the Pritchard and Gilad Labs for helpful discussions. We also thank the reviewers for their valuable comments and suggestions. This work was supported by NIH grants GM007197, AG 044948, MH084703, MH101825, HG007036, CA149145, and HL092206; by a Center for Computational, Evolutionary and Human Genomics Fellowship; by an EMBO Long-Term Fellowship (ALTF 751-2014) and Marie Curie Actions; and by the Howard Hughes Medical Institute.